Scientific Advances
- Biomass conversion efficiency
- Fermentation of grasses
- Fructan studies
- Miscanthus genetic resources
- Ryegrass biomass for ethanol production
- Willows
- Delayed senescence gene identified
- Grasses/cereals
- Genetic and growth analysis of highly diverse Lolium and Festuca cultivars
- Lolium molecular genetics
- Gene mapping
- Oats BAC library
- Clovers
- Mapping variation in water use efficiency in white clover
- Abiotic stress
- Red clover orthologous sequences
- Polyphenol oxidase genes in red clover
- Higher order regulatory mechanisms of polyphenolic accumulation in legumes and grasses
- Lolium-Festuca introgression
- Transformation Technologies Platform
- Water-soluble carbohydrates in grasses
Greenhouse gas emissions/Biogas
- UK Greenhouse Gas inventory
- UK Ammonia inventory
- Optimisation of anaerobic digestion for biogas production
- CO2 respiration following the application of different particle-size fractions separated
- SuperGrass
- Improved guidance on the use of fertility building crops in organic farming
- Nitrogen excretion on unimproved grasslands
- Potential for enhancing biodiversity on intensive livestock farms
- Nitrate leaching linked to aspects of soil quality
- Nutrient-use efficiency during soil-plant-animal interactions
- Phosphorus mobilisation with sediment and colloids through drained and undrained grasslands
- Seasonal variations in soil microbial phosphorus and P leaching to watercourses
Biomass and bioenergy
Biomass conversion efficiency:
Work continues on development of infrared spectroscopy for measuring elements of plant chemical composition likely to impact on biomass conversion efficiency. While the initial project focused on the use of model species, the current phase is now focusing on implementation with bioenergy crops such as Miscanthus. Two additional projects are looking at senescence and nitrogen mobilisation in Miscanthus and the chemical characterisation of fermentation of macroalgae. (Gordon Allison, Jessica Adams, Phil Morris, Iain Donnison)
Fermentation of grasses:
A Welsh Energy Research Centre (WERC)-funded project in collaboration with Swansea University has begun to assess the fermentability and processing capacity of forage grasses such as Lolium perenne as energy crops. (Mike Morris, Colin Jackson, Joe Gallagher, Iain Donnison)
Fructan studies:
Fructan exohydrolase activity for biomass fermentation is being characterised from a protein extraction of Lactobacillus. The enzymes involved have been purified and their amino acid sequences determined. Levanase, inulinase and sucrase activity levels have been identified with the use of IEF gels, levanase activity being predominant. (Ana Winters, Colin Jackson, Joe Gallagher)
Miscanthus genetic resources:
In a new 5-year BBSRC Institute Career Path Fellowship ‘Understanding and exploiting the diversity of form in Miscanthus’, plant architecture has been identified as important factor for biomass yield which is under genetic control. Mapping information from other grasses, model species and sugarcane will be used to identify candidate genes for cloning in Miscanthus with the aid of BAC libraries. (Kerrie Farrar). To develop the BAC library in Miscanthus for use in comparative genomic studies, DNA samples have been isolated from a range of Miscanthus genotypes, including a mapping population intended for molecular marker studies. (Paul Robson, Kerrie Farrar, Iain Donnison)
A Miscanthus mapping population has been created for the association of flowering phenotype to genotype through the mapping of maize simple sequence repeats (SSRs) which are known to co-locate to quantitative trait loci (QTL) for flowering time. An additional set of mapping crosses have also recently been developed to help to assess the impact of a greater number of alleles. (Elaine Jensen, Kerrie Farrar, Iain Donnison)
Phenotyping studies have been continuing in a long-term trait trial involving approximately 250 Miscanthus genotypes, looking to improve low cost establishment, total yield, inter-annual stability, persistence, stable composition and quality in this relatively undeveloped biomass crop. The Miscanthus collection is being supplemented by the addition of ‘Convention of Biological Diversity- compliant’ collections from Asia. (John Clifton-Brown)
Ryegrass biomass for ethanol production
In studies on hybrid-renewable saccharification and fermentation of pasture ryegrass biomass, preliminary characterisations have determined that saccharification of ryegrass for ethanol production is possible at process temperatures achievable with solar thermal energy. It was also found that a range of inhibitors of endomembrane function inhibited fructan polymerisation in leaves of Lolium temulentum. (Andy Cairns)
Willows:
A major effort has been made to produce a new economic model for short-rotation coppice willow, allowing the effects of varying price and yield to be examined. While gross margins based on a 16 year rotation compare well with those from livestock enterprises, the need for support mechanisms in the initial years was demonstrated. Following experimental results showing higher than expected biodiversity values from willow plantations, discussions with the Welsh Assembly Government have started on the possibilities for support from EC Axis 2 funds on the basis of new agri-environmental schemes for carbon mitigation, efficient use of resources AND increased biodiversity. (John Valentine)
A matrix is being produced looking at the potential of biomass raw materials for thermal conversion processing, specifically in relation to their physico-chemical properties and market traits. A 400t + co-firing trial of short-rotation coppice willow chips from the Willow for Wales project is being planned with RWEnpower at Aberthaw. (John Valentine)
Molecular genetics
Delayed senescence gene identified:
The identification of a key gene responsible for delayed senescence in Pisum sativum, Arabidopsis thaliana, and Festuca pratensis has been achieved by using a combination of classical and molecular genetics, paired with comparative genomics techniques. The gene identified was also found to be responsible for the green and yellow seed phenotype in pea, i.e. Mendel’s I locus. Different aspects of this major highlight in our genetics research were variously published in the New Phytologist and Science, receiving wide media publicity. (Ian Armstead, Ian King, Iain Donnison, John Harper, Caron James, Helen Ougham, Luned Roberts, Ann Thomas)
Grasses/Cereals
Genetic and growth analysis of highly diverse Lolium and Festuca cultivars:
In the BBSRC SuperGraSS project, detailed above- and below-ground growth analyses of highly diverse Lolium and Festuca cultivars have been carried out, incorporating both introgression lines and monosomic chromosome substitution lines. Results for irrigated conditions have then been compared with those for drought. The aim is to seek out single nucleotide polymorphisms (SNP’s) for candidate genes whose presence underlies quantitative trait loci (QTL) for rooting traits and drought resistance on Festuca and Lolium chromosome 3. The synteny of chromosome 3 along its entire length with rice chromosome 1 will allow future comparisons between these species. Quantitative trait loci (QTL) for rooting characters in Festuca species are also being compared with those found for water-soluble carbohydrates in a perennial ryegrass mapping population. (Mike Humphreys, Lesley Turner, Leif Skøt, Sarah Hawkins)
Lolium molecular genetics:
Work on Lolium substitution lines has progressed to the stage where genetic linkage maps based on microsatellite markers are now in place for six of the Lolium chromosomes, with work on the seventh well advanced. (Annals of Botany, in press). Related work on Lolium/Festuca introgression maps is currently underway, with experimental plants being selected on the basis of marker order for genomic in situ hybridisation.
The CSI grant award has been running since the beginning of March 2007. Primers have been designed from every 10th BAC on rice chromosomes 2-10 and the primers for the BACs on rice chromosomes 2-7 have been screened on the substitution lines. This has enabled us to start to establish the broad synteny between rice and Lolium/Festuca.
Initial work using Lolium/Festuca chromosome 3 as a prototype for demonstrating synteny with rice chromosomes was published in the September issue of Genetics. The work was also presented in invited papers at the ELFIN Molecular Breeding of Forage and Turf Conference in Sapporo in July 2007 (Julie King) and at the Eucarpia Fodder Crops and Amenity Grasses Symposium in Copenhagen in August 2007 (Ian King). A joint grant with JIC was started in the summer to develop cross species markers across a wide range of monocots based on this research.
A study of an unknown forage grass discovered growing in the shade of a remnant oak savanna in Wisconsin in 1990, is being carried out in collaboration with Mike Casler of the US Dairy Forage Research Center. A DNA comparison of this genetically highly diverse population with both Lolium and Festuca, using genomic in-situ hybridization (GISH) and genetic distance analysis, confirmed that the plants were most closely allied with F. pratensis. Sequence analysis distinguished the unknown plants from F. arundinacea but not from Lolium. Soil samples accompanying the plants indicated no seed banks and most farm records indicated no commercially introduced seeds during the 20th century. As such, it is hypothesised that seeds of meadow fescue (F. pratensis) may have arrived with some of the earliest European immigrants to Wisconsin and spread along the historic Military Ridge Trail, a network of frontier US Army forts connected by a major thoroughfare. (Mike Humphreys)
Gene mapping:
In silico approaches have provided a list of 680 candidate genes in Festuca relating to drought stress and root growth-related traits. Further searches against Lolium perenne expressed sequence tags (EST’s) and GeneThresher libraries will identify homologues in this species, enabling sequence comparison and SNP discovery for future use in marker assisted selection. (Leif Skøt)
Association mapping in Lolium perenne has led to the identification of a promising molecular marker associated closely with flowering time and linked to the photoperiod responsive gene LpHD1 (Skøt et al., 2007: Genetics 177, 535-547.). This has been confirmed by testing progeny arising from crosses between selected genotypes from the LD population with very late flowering genotypes of a turf grass variety. (Danny Thorogood, Leif Skøt)
Oats BAC library:
A partial BAC library of oats has been developed and used to isolate centromeric BACs (verified by FISH) which are then being sub-cloned and characterised further. Oat-maize chromosome addition lines are being used to screen for heterologous mobile element activity. The genetic map of hexaploid oats now has 130 loci and syntenic relationships with the diploid oat map have now been established. Markers closely linked to height and grain oil content have been identified and are currently being validated over a wider range of genetic material. Novel markers are currently in development to extend this map, with particularly promising results being obtained from the addition of Conserved Orthologous Sequence (COS) markers.
Clovers
Mapping variation in water use efficiency in white clover:
Techniques commonly used to measure water use efficiency (WUE) are appropriate for relatively small numbers of plants and, as such, they are usually inappropriate for studying the large number of specimens contained within a mapping family. In the past year, however, we have developed a simplified WUE technique suitable for use with such larger populations. Results from its application to quantify WUE variation in a white clover mapping family developed to study stolon architecture and root development will now be incorporated into processes to identify the relevant quantitative trait loci (QTL) in clover which underpin variation in WUE. (Athole Marshall)
Abiotic stress:
Identification of a water-stress related putative O-methyltransferase gene, encoding a cold-induced protein which is known to be expressed in both red and white clover, has led to BAC-clone identification in the red clover library. Both red and white clover genes will be mapped in the red clover F1 mapping family and used as candidate genes (together with others) in association mapping of abiotic stress. (Leif Skøt)
Red clover orthologous sequences:
In the ERANET-Plant Genetics project, more than 40 Conserved Orthologous Sequences (COS) have been identified in red clover and used in BAC library screening since April 2007. The objective is to obtain 150 markers anchored to BAC contigs, aligning them to both the Medicago truncatula genome and to the existing genetic map of red clover. (Leif Skøt)
Polyphenol oxidase genes in red clover:
Recent research in red clover has targeted polyphenol oxidase (PPO) genes, widely considered to play roles in both plant protection and feed quality. Screening of a BAC library of red clover DNA revealed eight different PPO genes, six of which appear to be clustered in one section of the genome. These sequences will be used to study PPO function in aerial and root tissues, as well as to identify genetic markers suitable for use in plant breeding studies. (Ana Winters, Judith Webb).
In addition a new PPO substrate, a caffeic acid isocitrate methyl ester, has been identified and isolated for the first time in cocksfoot (with Ifat Parveen).
Selecting genes for function
Higher order regulatory mechanisms of polyphenolic accumulation in legumes and grasses:
Work on TILLING for R2R3MYB genes regulating proanthocyanidin and isoflavonoid pathways in Lotus japonicus has been partially successful. Functional assessment was not possible owing to gene redundancy, one example being that 3 AtTT2 orthologues responsible for the regulation of proanthocyanidin biosynthesis were found in a tandem array. Following a visit to the 5th International Symposium on the Molecular Breeding of Forage and Turf (MBFT2007) in Sapporo, new strategies based upon RIKEN dominant-suppressor methodologies have been developed aiming for reducing the levels of lignin and cell wall phenolics in Miscanthus spp. (Mark Robbins)
Lolium-Festuca introgression:
Detailed analyses have been made of root development in Lolium, Festuca, and Festulolium cultivars, including an entire series of monosomic chromosome substitution lines and their parents, aiming to identify genes for increased root growth and penetration of hard soils. Grasses expressing such phenotypes would encourage increased soil porosity, reduce flooding during times of water surplus and enable access to deeper water during drought, As rice chromosome 1 contains a number of QTL’s associated with root growth and depth, it is expected that orthologous sequences may be found in Festuca lines with larger root systems. A catscan of soil cores revealed changes in soil structure and increased soil porosity in soils under F. arundinacea compared with Lolium. Better water-use-efficiency and root growth of F. arundinacea under irrigated and drought stress conditions compared to Lolium was demonstrated. (Mike Humphreys)
Research is being coordinated utilising Festulolium monosomic chromosome substitution lines and recombination series for use in Defra Plant Breeding programmes. (Mike Humphreys) The primary sites for identification of genes for improved nitrogen-use-efficiency (NUE) have been identified. (James Macduff)
Festuca genes identified for drought resistance and water-use-efficiency in the EU Framework 5 SAGES Project are now being incorporated into cultivar development as introgressions into Lolium multiflorum in the Plant Breeding and Genetics Programme. Further work will centre on transferring the introgressed genes to Lolium perenne.
Transformation Technologies Platform:
Brachypodium distachyon plantlets have been regenerated from cultures bombarded with a ferulic acid esterase (FAE) construct. Bombardment of these calli with a xylanase construct has also been studied (Phil Morris). New Miscanthus calli have been started from an amenable genotype and a number of non-GM regenerants planted out for study of survival and growth. Tetraploid and diploid Lolium multiflorum calli have been bombarded with the YFP gene under six fructan promoter constructs. (with Joe Gallagher). Festuca pratensis calli were bombarded with the staygreen complementation construct (Paul Robson). Agrobacterium-mediated transformation experiments have been carried out with a variety of cultures in order to improve efficiency (Sue Dalton).
Six Brachypodium distachyon plants - the four in the middle express an FAE construct and the two on the outside are controls.
Water-soluble carbohydrates in grasses:
Transformed Lolium plants containing transit peptides fused to Yellow Fluorescent Protein (YFP) have been analysed to determine the cellular location of invertases and fructosyltransferases (Sue Dalton). Expression profiles of invertases and fructosyltransferases are being studied under a range of treatments. We continue to isolate genes involved in carbohydrate metabolism, including a number of invertases from Miscanthus. Candidate genes are provided for mapping programmes (Lesley Turner).
Greenhouse gas emissions/Biogas
UK Greenhouse Gas inventory:
North Wyke has responsibility for compiling the UK Greenhouse Gas Inventory for the agricultural sector and for research aimed at disaggregating individual N2O emission factors. The accuracy of measurement and impact assessment has been improved through (i) new field-scale experimental data obtained from both grazed grassland and arable cropping sites with a range of soils and climates and (ii) utilisation of the UK-DNDC model to evaluate the impacts of potential N2O mitigation measures. Detailed mechanistic studies are being made using our laboratory soil incubation apparatus (DENIS) which measures biogenic emissions of greenhouse gases (GHGs). Relations between nitrification/denitrification processes with both soil structure and carbon cycling are being investigated using isotopomers and isotope analysis. Further emissions research using subsoils are to be carried out in collaboration with TEAGASC in Ireland. A Royal Society-funded project working with Chilean scientists is looking at natural inhibition of nitrification in low leaching volcanic soils.
UK Ammonia emissions inventory:
North Wyke also has responsibility for compiling the annual national UK inventory specifically for agricultural emissions of ammonia. Work is currently focused on increasing the robustness of input parameters and their ability to reflect spatial and temporal variation in the applied model. A User Manual for the model is being produced, describing the various techniques for mitigating ammonia emissions, their relative effectiveness and practical cost of implementation. The model is being used to identify the most cost-effective means of meeting national emissions targets set for ammonia by 2020 and, at a smaller scale, to look at local impact assessments and better targeting of mitigation policies.
Optimisation of anaerobic digestion for biogas production:
Taguchi methodology is being used to design laboratory experiments aimed at identifying key parameters important for anaerobic digestion process-control. Construction and equipping of a pilot-scale digester is nearing completion. Testing of Near Infrared Spectroscopy as a sensor for process-control is being investigated using digestate samples from Holsworthy Anaerobic Digestion Plant in Devon. Characterisation and measurement of the extracellular polymers produced by bacteria during the digestion process is underway, particularly assessing the role that these polymers may play in enhancing bacterial clumping and improving the potential for efficient biogas production. Collaborations with the Centre for Cellular and Molecular Biology in Hyderabad are being explored to enable identification and profiling of microbial communities and their survival under different conditions for biogas production. (Phil Hobbs)
Multi-fermentation configuration to determine optimum conditions for the production of biogas using factorial design.
CO2 respiration following the application of different particle size fractions separated from slurry to grassland soils:
Studies have been made of on-farm slurry separation aiming to extract organic matter with a range of particle sizes. When applied to the soil, different particle sizes of slurry organic matter have been shown to reduce or modify short-term CO2 emissions. (David Chadwick, Roland Bol and colleagues).
Grasslands
SuperGrass
The BBSRC Supergrass Project (BB/D011612/1) on “Exploiting genetic diversity in grasses to manage the biophysical interactions in grassland soils” has been highly successful in its first year, with the establishment of tightened hypotheses for experimentation and publication in a peer reviewed journal. Following extensive calibration procedures, field-based runoff plots have been set up on the Rowden Experimental Research Platform at North Wyke looking at the impact of six grasses on soil hydraulic functions using tension-infiltration measurements in collaboration with project colleagues from Rothamsted. (Phil Haygarth)
Improved guidance on the use of fertility building crops in organic farming
Whilst a net input of nitrogen on organic farms is achieved with N fixed by legumes in order to maintain soil fertility, this Defra-funded study showed that gains in soil nitrogen from application of FYM or green manures actually reduces the proportion of N fixed, compared with swards where the herbage is cut and removed. (Hatch et al., 2007. Bioresource Technology, 98, 3243-3248).
Nitrogen excretion on unimproved grasslands
Whilst many studies have examined N excretion from sheep/cattle on intensively managed swards, a recent Defra project at North Wyke has demonstrated that in a leniently-grazed unimproved grassland, the proportion of ingested N excreted as urine is greatly reduced. This has implications both for botanical diversity and for the balance of pathways by which N losses occur. (Project LS3659: Optimising nutrient use efficiency in beef cattle grazing lowland semi-natural pastures) (Robert Orr)
Potential for enhancing biodiversity on intensive livestock farms
This Defra-funded project demonstrated that grass field margins can be managed to improve the faunal diversity of intensive lowland grassland (Woodcock et al., 2007. Journal of Applied Ecology 44, 60-69) (Jerry Tallowin)
Soils
Nitrate leaching linked to aspects of soil quality
Two field experiments investigating potential links between nitrate leaching and aspects of soil quality were carried out, utilising both legume-based mixtures and legume monocultures. Results suggest that the inclusion of additional plant functional groups within complex legume mixtures might reduce nitrate leaching, providing that an appropriate species balance is maintained. In order to test evidence that legumes can enhance soil porosity as one parameter of soil quality, a novel oxygen diffusivity technique was used as a measure soil porosity in experiments comparing grass and legume plots. The ranking order of the species in terms of soil porosity (red clover> white clover> cocksfoot) reflected that for nitrate leaching, which is suggestive of some association. (Rosemary Collins)
Trials plots with apparatus for measuring nitrate leaching sticking out of the soil
Nutrient-use efficiency during soil-plant-animal interactions
Novel approaches have been devised for studies looking to maximise the nutrient-use efficiency of soil-plant-animal interactions, aiming to reduce the environmental impact of livestock systems. Outcomes of collaborative research at both Aberystwyth and North Wyke have included: demonstrating a need to revise the current Defra fertiliser guidelines to optimise nutrient use by different forage crops; ideas for mitigating emissions of nitrous oxide from slurry by altering ruminant diets; and highlighting the potential for red clover to reduce farm-gate phosphorus balances. (Christina Marley)
Phosphorus mobilisation with sediment and colloids through drained and undrained grasslands
Investigations of the dynamics and mass balances of sheet erosion from drained and undrained grasslands (with P and C attached) have taken place as part of the Defra GRASP Project (PE020). New technologies are being developed to separate the colloidal fractions in soil runoff and to undertake isotopic tracing studies to develop a mechanistic model of colloidal P transfer as a research tool. (Phil Haygarth)
Seasonal variations in soil microbial phosphorus and P leaching to watercourses
A major investigation of the spatial heterogeneity of total soil C, N and P in comparison with microbial P variation in the Rowden Plots has been completed as part of the second-year experiments in the BBSRC-funded (BB/C504919/1) project. At the smaller 1m2 lysimeter scale, experiments on the effects of two irrigation regimes on P dynamics have been compared on bare and planted soils. (Phil Haygarth)